Re: [gmx-users] generating movie file

[Justin Lemkul]

On 1/27/18 7:12 AM, Vidya R wrote:

I want to include the movie file in my ppt (using MS office).


Rendering a movie requires you to create some useful representation of 
the system, color properly, add labels to things or represent whatever 
is meaningful, then encode that in a movie format. None of that can be 
done in GROMACS. Please consult the various tutorials available for 
visual rendering programs and ask questions in the appropriate forum.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Replica exchange checkpoint error

[金 瑞涛]

Hello Mark

It makes sense to me , I have already restarted my simulations, hopefully it 
will write up cpt as it supposed to do.

Best regards

Riotto



Sent from my Samsung Galaxy smartphone.


 Original message 
From: Mark Abraham 
Date: 28/1/18 1:17 am (GMT+10:00)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Replica exchange checkpoint error

Hi,

They got opened immediately. Fifteen minutes before the checkpoint file.

Mark

On Sat, Jan 27, 2018, 15:09 金 瑞涛  wrote:

> Hello Mark
>
> Thanks for repling me, i am wondering if it is file system problem, why
> the other files like trr, xtc and log file were still updated?
>
> Best regards
>
> Riotto
>
>
>
> Sent from my Samsung Galaxy smartphone.
>
>
>  Original message 
> From: Mark Abraham 
> Date: 28/1/18 12:47 am (GMT+10:00)
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Replica exchange checkpoint error
>
> Hi,
>
> That sounds most likely a file system has decided to go missing by the time
> the first checkpoint file is written after fifteen minutes. As such, all
> you can do is try again and complain to the cluster admins if it keeps
> happening.
>
> Mark
>
> On Fri, Jan 26, 2018, 04:09 金 瑞涛  wrote:
>
> > Dear Gromacs users and developers
> >
> >
> > I am currently facing a problem from one of my simulations. I am doing
> > replica exchange simulation which has 48 subsystems, when I started the
> > simulation, everything wss fine, but when I restarted them from
> checkpoint
> > file, they looked running, were keeping generating log file, trr file,
> edr
> > file, etc, but not checkpoint file were generated at all.
> >
> >
> > The version I am using is gromacs/5.1.3, any idea what is going wrong
> with
> > simulations of grimaces?
> >
> >
> > Best regards
> >
> >
> > Riotto
> >
> >
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
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Re: [gmx-users] Replica exchange checkpoint error

[Mark Abraham]

Yes

On Sat, Jan 27, 2018, 15:10 金 瑞涛  wrote:

> Hello Dhaniram
>
> Thanks for repling me! Is -append option a default option?
>
> Best regards
>
> Riotto
>
>
>
> Sent from my Samsung Galaxy smartphone.
>
>
>  Original message 
> From: Dhaniram Mahato 
> Date: 27/1/18 3:14 pm (GMT+10:00)
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Replica exchange checkpoint error
>
> you can try by adding this line in your mdrun_mpi command.
>
> mdrun_mpi -s topol.tpr -cpi state.cpt -append -multi 48 
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Re: [gmx-users] Replica exchange checkpoint error

[Mark Abraham]

Hi,

They got opened immediately. Fifteen minutes before the checkpoint file.

Mark

On Sat, Jan 27, 2018, 15:09 金 瑞涛  wrote:

> Hello Mark
>
> Thanks for repling me, i am wondering if it is file system problem, why
> the other files like trr, xtc and log file were still updated?
>
> Best regards
>
> Riotto
>
>
>
> Sent from my Samsung Galaxy smartphone.
>
>
>  Original message 
> From: Mark Abraham 
> Date: 28/1/18 12:47 am (GMT+10:00)
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Replica exchange checkpoint error
>
> Hi,
>
> That sounds most likely a file system has decided to go missing by the time
> the first checkpoint file is written after fifteen minutes. As such, all
> you can do is try again and complain to the cluster admins if it keeps
> happening.
>
> Mark
>
> On Fri, Jan 26, 2018, 04:09 金 瑞涛  wrote:
>
> > Dear Gromacs users and developers
> >
> >
> > I am currently facing a problem from one of my simulations. I am doing
> > replica exchange simulation which has 48 subsystems, when I started the
> > simulation, everything wss fine, but when I restarted them from
> checkpoint
> > file, they looked running, were keeping generating log file, trr file,
> edr
> > file, etc, but not checkpoint file were generated at all.
> >
> >
> > The version I am using is gromacs/5.1.3, any idea what is going wrong
> with
> > simulations of grimaces?
> >
> >
> > Best regards
> >
> >
> > Riotto
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Replica exchange checkpoint error

[金 瑞涛]

Hello Dhaniram

Thanks for repling me! Is -append option a default option?

Best regards

Riotto



Sent from my Samsung Galaxy smartphone.


 Original message 
From: Dhaniram Mahato 
Date: 27/1/18 3:14 pm (GMT+10:00)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Replica exchange checkpoint error

you can try by adding this line in your mdrun_mpi command.

mdrun_mpi -s topol.tpr -cpi state.cpt -append -multi 48 
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Re: [gmx-users] Replica exchange checkpoint error

[金 瑞涛]

Hello Mark

Thanks for repling me, i am wondering if it is file system problem, why the 
other files like trr, xtc and log file were still updated?

Best regards

Riotto



Sent from my Samsung Galaxy smartphone.


 Original message 
From: Mark Abraham 
Date: 28/1/18 12:47 am (GMT+10:00)
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Replica exchange checkpoint error

Hi,

That sounds most likely a file system has decided to go missing by the time
the first checkpoint file is written after fifteen minutes. As such, all
you can do is try again and complain to the cluster admins if it keeps
happening.

Mark

On Fri, Jan 26, 2018, 04:09 金 瑞涛  wrote:

> Dear Gromacs users and developers
>
>
> I am currently facing a problem from one of my simulations. I am doing
> replica exchange simulation which has 48 subsystems, when I started the
> simulation, everything wss fine, but when I restarted them from checkpoint
> file, they looked running, were keeping generating log file, trr file, edr
> file, etc, but not checkpoint file were generated at all.
>
>
> The version I am using is gromacs/5.1.3, any idea what is going wrong with
> simulations of grimaces?
>
>
> Best regards
>
>
> Riotto
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

[金 瑞涛]

Hello

Have you tried different pressure coupling type? Maybe a semi-isotropic one 
will solve the problem if you chose z-axis as your pulling vector direction.

Best regards

Riotto



Sent from my Samsung Galaxy smartphone.


 Original message 
From: Shrinath Kumar 
Date: 28/1/18 12:53 am (GMT+10:00)
To: gmx-us...@gromacs.org
Subject: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 
times box size error

Hi,

I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big nor can
I use pull-geometry = direction-periodic as I need to use NPT.

But I'm confused on why I get this error in the first place because my
periodic box is a cuboid and the pulling distance is less than 0.5*box size
in each dimension. So the pulling vector should be uniquely determined and
there should be no discontinuities.

To solve this I tried having 3 pull coordinates each acting on a separate
dimension. This solves the grompp error. But would this produce the same
results as having 1 pull coordinate acting on all 3 dimensions? Or is there
any better workaround for this?

Thanks,
Shrinath
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Re: [gmx-users] Compiling Gromacs 2018 using Intel 2018.1 compiler on OSX 10.13.3

[Mark Abraham]

Hi,

We haven't tried to build with icc on Mac, but as you say the problem is
likely with that version of icc there. The icc 18 compiler works fine on
Linux and Windows... Check for an updated version, or use gcc.

Mark

On Fri, Jan 26, 2018, 18:32 Zhiyi Wu  wrote:

> Hi,
> I’m trying to compile Gromacs 2018 with icc 2018.1.126 on a iMac using flag
>
> cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_GPU=on
> -DGMX_USE_OPENCL=on -DGMX_SIMD=AVX2_256 -DGMX_FFT_LIBRARY=mkl
> -DREGRESSIONTEST_DOWNLOAD=ON
>
> The cmake succeed without any warning but during the making I have
> encountered an error.
>
> [ 23%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o
> /Users/zhiyiwu/src/gromacs-2018/src/gromacs/gmxana/gmx_dipoles.cpp(257):
> error: expected an identifier
>   if (debug || std::isnan(cosa))
> compilation aborted for
> /Users/zhiyiwu/src/gromacs-2018/src/gromacs/gmxana/gmx_dipoles.cpp (code 2)
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o] Error 2
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> I have repeated the same compilation on another Mac and encountered the
> same error. I have tried to replace icc with GCC7 and the compilation
> succeed without any error. I have also tried to compile the same Gromacs on
> a Linux with the same 2018.1 intel compiler (2018.1.163) and it succeeded
> without any error.
> It seems that this error only occurred when using icc on a Mac. I wonder
> if there is any way of solving this problem? Thanks,
> Kind regards,
> Zhiyi Wu
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[gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

[Shrinath Kumar]

Hi,

I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big nor can
I use pull-geometry = direction-periodic as I need to use NPT.

But I'm confused on why I get this error in the first place because my
periodic box is a cuboid and the pulling distance is less than 0.5*box size
in each dimension. So the pulling vector should be uniquely determined and
there should be no discontinuities.

To solve this I tried having 3 pull coordinates each acting on a separate
dimension. This solves the grompp error. But would this produce the same
results as having 1 pull coordinate acting on all 3 dimensions? Or is there
any better workaround for this?

Thanks,
Shrinath
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Re: [gmx-users] Using libgromacs in a CMake project built on the fly?

[Mark Abraham]

Hi,

In theory, one can compose CMake projects like that, but we have not tried
to make that work with GROMACS. A better approach is probably to use a
CMake external project to build GROMACS and thereby install it into the
build tree. That installation has a FindGROMACS.cmake file that your main
project can be told to use.

Mark

On Sat, Jan 27, 2018, 04:12 Cory J. Geesaman  wrote:

> Is it possible to use libgromacs in a CMake based project which links the
> library in at build time (but from source as opposed to a system-wide
> installation?)
>
>
>
> So far I have the gromacs source included as a submodule from
> https://github.com/gromacs/gromacs.git located in the subdirectory
> 3rdparty/gromacs/
>
>
>
> In my CMakeLists.txt I have:
>
>
>
>
> include_directories(${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/gromacs/src/gromacs
> )
>
>
>
> and a bit further down:
>
>
>
> target_link_libraries(${PROJECT_NAME} ${Boost_LIBRARIES} libgromacs)
>
>
>
> Which seems to pass the CMake tests, but when it gets to actually building
> the project I get the error:
>
>
>
>
> c:/progra~1/mingw/bin/../lib/gcc/x86_64-w64-mingw32/7.2.0/../../../../x86_64
> -w64-mingw32/bin/ld.exe: cannot find -llibgromacs
>
> collect2.exe: error: ld returned 1 exit status
>
>
>
> I'm sure this is some kind of CMake error but I don't know what it could be
> precisely because I'm relatively new to CMake.  I'm building with
> CLion+MinGW on Windows 7 (but also intend to build on Linux.)
>
>
>
> Additionally, are there any significant gromacs-specific performance
> concerns I should be aware of building Windows binaries with MinGW or will
> it work as well as with a Windows build platform like visual c++?
>
>
>
> Thanks for any information,
>
> Cory
>
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Re: [gmx-users] Replica exchange checkpoint error

[Mark Abraham]

Hi,

That sounds most likely a file system has decided to go missing by the time
the first checkpoint file is written after fifteen minutes. As such, all
you can do is try again and complain to the cluster admins if it keeps
happening.

Mark

On Fri, Jan 26, 2018, 04:09 金 瑞涛  wrote:

> Dear Gromacs users and developers
>
>
> I am currently facing a problem from one of my simulations. I am doing
> replica exchange simulation which has 48 subsystems, when I started the
> simulation, everything wss fine, but when I restarted them from checkpoint
> file, they looked running, were keeping generating log file, trr file, edr
> file, etc, but not checkpoint file were generated at all.
>
>
> The version I am using is gromacs/5.1.3, any idea what is going wrong with
> simulations of grimaces?
>
>
> Best regards
>
>
> Riotto
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] generating movie file

[Vidya R]

I want to include the movie file in my ppt (using MS office).



On Sat, Jan 27, 2018 at 11:19 AM, Alex  wrote:

> No, there are other tools for that (e.g. pymol + avidemux).
>
> I too was wondering if trjconv could produce an mp4 and add Morgan
> Freeman's voice as narration to my glorious trajectory, but was
> disappointed. Very useful for supplemental files for journals with IF>10.
> Maybe gmx developers should look into that.
>
>
>
> On 1/26/2018 9:51 PM, Vidya R wrote:
>
>> Hi gromacs users,
>>
>>
>> Can we generate .mp4 file instead of .pdb using gmx trjconv?
>>
>> Thanks,
>> Vidya.R
>>
>
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